Michael,
Just have patience. Practice a few measures at a time - hands alone, together - and I also have found helpful with Bach - play the sections that give you the most trouble hands alone but do different "beat" patterns like long, short, long, short (1st note long, second note short etc). Change which notes get the emphasis - every 3rd, every 4th etc.
The theory behind this is that if you can play it in a "difficult" way, playing it correctly will become easier. This also helps with uneven playing. Don't know if I'm making sense - sorry.
Sometimes I find it just takes a while before you "get it". Bach is my favorite - and over the years I have had up and down experiences when learning his pieces. I have also had this experience when teaching his pieces!
Working on a concerto right now and I can't practice every day like I would like to. But I know I'll get there eventually.
Hang in there